SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    125768, 125767, 125766, 125765, 125764, 
    125763, 125762, 125761, 125760, 125759, 
    125758, 125757, 125756, 125755, 125754, 
    125753, 125752, 125751, 125750, 125749, 
    125748, 125747, 125746, 125745, 125744
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00083

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id usergroup 9 50 Using where

Result

product_id price
125744 1.69000000
125745 1.69000000
125746 1.69000000
125747 1.69000000
125748 1.69000000
125749 1.69000000
125750 1.69000000
125751 1.69000000
125752 1.69000000
125753 1.69000000
125754 1.69000000
125755 1.69000000
125756 1.69000000
125757 1.69000000
125758 1.69000000
125759 1.69000000
125760 1.69000000
125761 1.69000000
125762 1.69000000
125763 1.69000000
125764 1.69000000
125765 1.69000000
125766 1.69000000
125767 1.69000000
125768 1.69000000